January 29, 2018

Breakthrough leads to sequencing of a human genome using a pocket-sized device  

Jared Simpson with MinION sequencer

A new nanopore technology for direct sequencing of long strands of DNA has resulted in the most complete human genome ever assembled with a single technology, scientists have revealed.

The research, published today in Nature Biotechnology, involved scientists from the University of Nottingham, University of Birmingham and the University of East Anglia in the UK; UC Santa Cruz at the University of California, Genome Informatics Section of the NIH and the University of Salt Lake City in the USA; and the University of British Columbia and the Ontario Institute for Cancer Research in Canada.

Using an emerging technology – a pocket sized, portable DNA sequencer – the scientists sequenced a complete human genome, in fragments hundreds of times larger than usual, enabling new biological insights.

Continue reading – Breakthrough leads to sequencing of a human genome using a pocket-sized device  

May 3, 2016

Tracking Ebola with portable sequencers

Could this technology be the key to monitoring the spread of Zika?

Jared Simpson with MinION sequencer

As West Africa was dealing with a massive outbreak of the Ebola virus, a group of researchers answered the call for assistance with a palm-sized device. Dr. Nick Loman and Mr. Josh Quick from the Institute of Microbiology and Infection at the University of Birmingham in the U.K., together with the help of OICR Investigator Dr. Jared Simpson, developed a ‘genome sequencing lab in a suitcase’ based around the tiny MinION sequencer. It was deployed to Conakry, Guinea in April of 2015 to test Ebola samples in the field.

Continue reading – Tracking Ebola with portable sequencers

February 3, 2016

Real time outbreak surveillance using genomics now possible in resource-limited conditions

New research published in Nature has shown how genome sequencing can be rapidly established to monitor outbreaks.

Dr. Simpson.TORONTO, Feb. 3, 2016 /CNW/ – Researchers designed a “genome sequencing laboratory in a suitcase”, employing a novel DNA sequencer, transporting the equipment in less than 50kg of airline luggage. This was initially deployed in Conakry, Guinea in April 2015 where Ebola samples from patients could be sequenced as soon as new cases were diagnosed. This reduced delays shipping to traditional genome laboratories often located on a different continent. The team found that they could generate sequencing information in as little as 24 hours after receiving a sample, with the sequencing process taking less than an hour.

Continue reading – Real time outbreak surveillance using genomics now possible in resource-limited conditions

June 15, 2015

Researchers sequence and assemble first full genome of a living organism using technology the size of smartphone

TORONTO, ON (June 15, 2015) Researchers in Canada and the U.K. have for the first time sequenced and assembled de novo the full genome of a living organism, the bacteria Escherichia Coli, using Oxford Nanopore’s MinIONTM device, a genome sequencer that can fit in the palm of your hand.

The findings, which were published today in the journal Nature Methods, provide proof of concept for the technology and the methods lay the groundwork for using it to sequence genomes in increasingly more complex organisms, eventually including humans, said Dr. Jared Simpson, Principal Investigator at the Ontario Institute for Cancer Research and a lead author on the study.

“The amazing thing about this device is that it is many times smaller than a normal sequencer – you just attach it to a laptop using a USB cable,” said Simpson. “And while our work is a demonstration of the capabilities of the technology, the most significant advance is in the methods. We were able to mathematically model nanopore sequencing and develop ways to reconstruct complete genomes off this tiny sequencer.”

While standard sequencing platforms can either generate vast amounts of data, or read long enough stretches of the genome to allow complete reconstruction, the Nanopore device has the potential to achieve both goals according to Simpson. “Long reads are necessary to assemble the most repetitive parts of genomes but we need a lot of reads if we want to sequence human genomes. The small size of the MinION suggests there is room to scale up and sequence larger and more complex samples,” Simpson said.

A drawback of the technology is that the single reads it produces are currently much less accurate than the reads produced by larger devices. Strong bioinformatics tools are needed to correct errors. The methods Simpson and colleagues developed are able to overcome the error rate and compute a more accurate final sequence.

“This was a fantastic example of a successful long distance research collaboration between Canada and the U.K.,” said Dr. Nicholas Loman, a co-lead author on the paper and an Independent Research Fellow from the Institute of Microbiology and Infection at University of Birmingham. “We explored new ways of working, including hosting a hackathon to explore new algorithm development and using shared computing resources on the Medical Research Council funded Cloud Infrastructure for Microbial Bioinformatics (CLIMB) based in the U.K. Midlands and Wales.”

The method of assembly the authors devised had three stages. First, overlaps between sequence reads are detected and corrected using a multiple alignment process. Then the corrected reads are assembled using the Celera assembler and finally the assembly is refined using a probabilistic model of the electric signals caused by DNA moving through the nanopore.

“This work has incredible potential,” said Dr. Tom Hudson, President and Scientific Director of the Ontario Institute for Cancer Research. “Scaled up, this technology could one day be used to sequence tumour genomes. The device’s portable nature would allow for sequencing to become far more accessible, bringing the option of more personalized diagnosis and treatment to more patients.”